Question: list of genes with associated histone marks
3
gravatar for Noyk
4.9 years ago by
Noyk50
Singapore
Noyk50 wrote:

Hi,

I would like to make association study between DNA methylation data with histone methylation.

Is there a processed list of genes with H3K4me3, H3K9me3, H3K27me3 and H3K36me3 marks in promoters or gene bodies?

chip-seq • 1.4k views
ADD COMMENTlink modified 4.9 years ago by Ming Tang2.5k • written 4.9 years ago by Noyk50
1

Which organism? Which developmental point? Which tissue? 

ADD REPLYlink written 4.9 years ago by Jelena Aleksic900
0
gravatar for PoGibas
4.9 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Noyk, you can use UCSC genome browser to get this data.

For example: select wanted histone modification (from "Table Browser -> Regulation -> SYDH Histone")
and use intersection with Genes group.


This way is simple and quick - should work for primary investigation.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by PoGibas4.8k
0
gravatar for Ming Tang
4.9 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

or if you have a bed peak file, you can use http://broad-enrich.med.umich.edu/

to annotate the peaks.

or you can download the refgene table from UCSC, get the promoter region for each gene, and use bedtools intersect with the histone modification peaks.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Ming Tang2.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1518 users visited in the last hour